GromacsTopFile Class Reference

GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it. More...

List of all members.

Classes
class	_MoleculeType
	## Inner class to store information about a molecule type.
Public Member Functions
def	__init__
	Load a top file.
def	createSystem
	Construct an OpenMM System representing the topology described by this prmtop file.
Public Attributes
	topology
	The Topology read from the prmtop file.

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Detailed Description

GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it.

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Constructor & Destructor Documentation

def __init__	(		self,
			file,
			periodicBoxVectors = None,
			unitCellDimensions = None,
			includeDir = None,
			defines = None
	)

Load a top file.

Parameters:

file	(str) the name of the file to load
periodicBoxVectors	(tuple of Vec3=None) the vectors defining the periodic box
unitCellDimensions	(Vec3=None) the dimensions of the crystallographic unit cell. For non-rectangular unit cells, specify periodicBoxVectors instead.
includeDir	(string=None) A directory in which to look for other files included from the top file. If not specified, we will attempt to locate a gromacs installation on your system. When gromacs is installed in /usr/local, this will resolve to /usr/local/gromacs/share/gromacs/top
defines	(dict={}) preprocessor definitions that should be predefined when parsing the file

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Member Function Documentation

def createSystem	(		self,
			nonbondedMethod = ff.NoCutoff,
			nonbondedCutoff = 1.0*unit.nanometer,
			constraints = None,
			rigidWater = True,
			implicitSolvent = None,
			soluteDielectric = 1.0,
			solventDielectric = 78.5,
			ewaldErrorTolerance = 0.0005,
			removeCMMotion = True,
			hydrogenMass = None
	)

Construct an OpenMM System representing the topology described by this prmtop file.

Parameters:

nonbondedMethod	(object=NoCutoff) The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
nonbondedCutoff	(distance=1*nanometer) The cutoff distance to use for nonbonded interactions
constraints	(object=None) Specifies which bonds and angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
rigidWater	(boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
implicitSolvent	(object=None) If not None, the implicit solvent model to use. The only allowed value is OBC2.
soluteDielectric	(float=1.0) The solute dielectric constant to use in the implicit solvent model.
solventDielectric	(float=78.5) The solvent dielectric constant to use in the implicit solvent model.
ewaldErrorTolerance	(float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
removeCMMotion	(boolean=True) If true, a CMMotionRemover will be added to the System
hydrogenMass	(mass=None) The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.

Returns:

(System) the newly created System

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Member Data Documentation

topology

The Topology read from the prmtop file.

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The documentation for this class was generated from the following file:

• gromacstopfile.py